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/* |
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* @version 1.0 |
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*/ |
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#include <sprng.h> |
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#include "brains/MoleculeCreator.hpp" |
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#include "brains/SimCreator.hpp" |
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#include "brains/SimSnapshotManager.hpp" |
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#include "UseTheForce/ForceFieldFactory.hpp" |
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#include "utils/simError.h" |
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#include "utils/StringUtils.hpp" |
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#include "math/SeqRandNumGen.hpp" |
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#ifdef IS_MPI |
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#include "io/mpiBASS.h" |
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#include "math/randomSPRNG.hpp" |
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#include "math/ParallelRandNumGen.hpp" |
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#endif |
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namespace oopse { |
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void SimCreator::parseFile(const std::string mdFileName, MakeStamps* stamps, Globals* simParams){ |
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void SimCreator::parseFile(const std::string mdFileName, MakeStamps* stamps, |
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Globals* simParams){ |
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#ifdef IS_MPI |
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if (worldRank == 0) { |
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#endif // is_mpi |
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simParams->initalize(); |
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set_interface_stamps(stamps, simParams); |
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simParams->initalize(); |
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set_interface_stamps(stamps, simParams); |
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#ifdef IS_MPI |
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mpiEventInit(); |
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mpiEventInit(); |
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#endif |
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yacc_BASS(mdFileName.c_str()); |
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yacc_BASS(mdFileName.c_str()); |
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#ifdef IS_MPI |
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throwMPIEvent(NULL); |
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throwMPIEvent(NULL); |
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} else { |
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set_interface_stamps(stamps, simParams); |
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mpiEventInit(); |
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MPIcheckPoint(); |
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mpiEventLoop(); |
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set_interface_stamps(stamps, simParams); |
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mpiEventInit(); |
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MPIcheckPoint(); |
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mpiEventLoop(); |
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} |
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#endif |
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} |
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SimInfo* SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) { |
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} |
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SimInfo* SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) { |
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|
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MakeStamps * stamps = new MakeStamps(); |
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Globals * simParams = new Globals(); |
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//parse meta-data file |
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parseFile(mdFileName, stamps, simParams); |
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|
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//create the force field |
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ForceField * ff = ForceFieldFactory::getInstance()->createForceField( |
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simParams->getForceField()); |
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simParams->getForceField()); |
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if (ff == NULL) { |
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sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n", |
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simParams->getForceField()); |
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painCave.isFatal = 1; |
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simError(); |
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sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n", |
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simParams->getForceField()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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if (simParams->haveForceFieldFileName()) { |
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ff->setForceFieldFileName(simParams->getForceFieldFileName()); |
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ff->setForceFieldFileName(simParams->getForceFieldFileName()); |
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} |
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std::string forcefieldFileName; |
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forcefieldFileName = ff->getForceFieldFileName(); |
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if (simParams->haveForceFieldVariant()) { |
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//If the force field has variant, the variant force field name will be |
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//Base.variant.frc. For exampel EAM.u6.frc |
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std::string variant = simParams->getForceFieldVariant(); |
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std::string::size_type pos = forcefieldFileName.rfind(".frc"); |
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variant = "." + variant; |
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if (pos != std::string::npos) { |
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forcefieldFileName.insert(pos, variant); |
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} else { |
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//If the default force field file name does not containt .frc suffix, just append the .variant |
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forcefieldFileName.append(variant); |
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} |
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//If the force field has variant, the variant force field name will be |
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//Base.variant.frc. For exampel EAM.u6.frc |
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|
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std::string variant = simParams->getForceFieldVariant(); |
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|
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std::string::size_type pos = forcefieldFileName.rfind(".frc"); |
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variant = "." + variant; |
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if (pos != std::string::npos) { |
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forcefieldFileName.insert(pos, variant); |
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} else { |
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//If the default force field file name does not containt .frc suffix, just append the .variant |
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forcefieldFileName.append(variant); |
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} |
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} |
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ff->parse(forcefieldFileName); |
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//extract the molecule stamps |
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std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs; |
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compList(stamps, simParams, moleculeStampPairs); |
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//create SimInfo |
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SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams); |
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SimInfo * info = new SimInfo(stamps, moleculeStampPairs, ff, simParams); |
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//gather parameters (SimCreator only retrieves part of the parameters) |
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gatherParameters(info, mdFileName); |
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//divide the molecules and determine the global index of molecules |
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#ifdef IS_MPI |
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divideMolecules(info); |
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#endif |
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|
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//create the molecules |
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createMolecules(info); |
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//allocate memory for DataStorage(circular reference, need to break it) |
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info->setSnapshotManager(new SimSnapshotManager(info)); |
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//global index will never change again). Local indices of atoms and rigidbodies are already set by |
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//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager. |
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setGlobalIndex(info); |
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//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point |
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//atoms don't have the global index yet (their global index are all initialized to -1). |
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//Therefore we have to call addExcludePairs explicitly here. A way to work around is that |
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SimInfo::MoleculeIterator mi; |
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Molecule* mol; |
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for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
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info->addExcludePairs(mol); |
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info->addExcludePairs(mol); |
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} |
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//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as |
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//eta, chi for NPT integrator) |
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if (loadInitCoords) |
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loadCoordinates(info); |
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loadCoordinates(info); |
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return info; |
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} |
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void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) { |
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|
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//setup seed for random number generator |
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int seedValue; |
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Globals * simParams = info->getSimParams(); |
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if (simParams->haveSeed()) { |
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seedValue = simParams->getSeed(); |
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|
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if (seedValue < 100000000 ) { |
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sprintf(painCave.errMsg, |
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"Seed for sprng library should contain at least 9 digits\n" |
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"OOPSE will generate a seed for user\n"); |
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painCave.isFatal = 0; |
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simError(); |
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//using seed generated by system instead of invalid seed set by user |
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#ifndef IS_MPI |
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seedValue = make_sprng_seed(); |
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#else |
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if (worldRank == 0) { |
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seedValue = make_sprng_seed(); |
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} |
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MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
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#endif |
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} //end if (seedValue /1000000000 == 0) |
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} else { |
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#ifndef IS_MPI |
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seedValue = make_sprng_seed(); |
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#else |
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if (worldRank == 0) { |
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seedValue = make_sprng_seed(); |
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} |
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MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
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#endif |
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|
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} //end of simParams->haveSeed() |
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info->setSeed(seedValue); |
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} |
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|
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void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) { |
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|
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//figure out the ouput file names |
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std::string prefix; |
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#ifdef IS_MPI |
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|
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if (worldRank == 0) { |
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#endif // is_mpi |
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if (simParams->haveFinalConfig()) { |
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prefix = getPrefix(simParams->getFinalConfig()); |
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} else { |
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prefix = getPrefix(mdfile); |
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} |
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info->setFinalConfigFileName(prefix + ".eor"); |
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info->setDumpFileName(prefix + ".dump"); |
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info->setStatFileName(prefix + ".stat"); |
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|
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Globals * simParams = info->getSimParams(); |
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if (simParams->haveFinalConfig()) { |
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prefix = getPrefix(simParams->getFinalConfig()); |
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} else { |
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prefix = getPrefix(mdfile); |
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} |
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|
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info->setFinalConfigFileName(prefix + ".eor"); |
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info->setDumpFileName(prefix + ".dump"); |
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info->setStatFileName(prefix + ".stat"); |
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info->setRestFileName(prefix + ".zang"); |
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|
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#ifdef IS_MPI |
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|
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} |
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#endif |
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} |
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|
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} |
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|
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#ifdef IS_MPI |
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void SimCreator::divideMolecules(SimInfo *info) { |
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void SimCreator::divideMolecules(SimInfo *info) { |
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double numerator; |
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double denominator; |
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double precast; |
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int which_proc; |
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int nProcessors; |
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std::vector<int> atomsPerProc; |
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randomSPRNG myRandom(info->getSeed()); |
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int nGlobalMols = info->getNGlobalMolecules(); |
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std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition: |
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|
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MPI_Comm_size(MPI_COMM_WORLD, &nProcessors); |
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|
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|
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if (nProcessors > nGlobalMols) { |
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sprintf(painCave.errMsg, |
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"nProcessors (%d) > nMol (%d)\n" |
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"\tThe number of processors is larger than\n" |
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"\tthe number of molecules. This will not result in a \n" |
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"\tusable division of atoms for force decomposition.\n" |
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"\tEither try a smaller number of processors, or run the\n" |
247 |
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"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols); |
248 |
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|
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painCave.isFatal = 1; |
250 |
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simError(); |
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sprintf(painCave.errMsg, |
242 |
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"nProcessors (%d) > nMol (%d)\n" |
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"\tThe number of processors is larger than\n" |
244 |
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"\tthe number of molecules. This will not result in a \n" |
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"\tusable division of atoms for force decomposition.\n" |
246 |
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"\tEither try a smaller number of processors, or run the\n" |
247 |
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"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols); |
248 |
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|
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painCave.isFatal = 1; |
250 |
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simError(); |
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} |
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|
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|
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int seedValue; |
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Globals * simParams = info->getSimParams(); |
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SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator |
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if (simParams->haveSeed()) { |
257 |
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seedValue = simParams->getSeed(); |
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myRandom = new SeqRandNumGen(seedValue); |
259 |
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}else { |
260 |
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myRandom = new SeqRandNumGen(); |
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} |
262 |
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|
263 |
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|
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a = 3.0 * nGlobalMols / info->getNGlobalAtoms(); |
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|
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|
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//initialize atomsPerProc |
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atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0); |
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|
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|
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if (worldRank == 0) { |
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numerator = info->getNGlobalAtoms(); |
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denominator = nProcessors; |
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precast = numerator / denominator; |
273 |
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nTarget = (int)(precast + 0.5); |
274 |
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|
275 |
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for(i = 0; i < nGlobalMols; i++) { |
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done = 0; |
277 |
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loops = 0; |
278 |
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|
279 |
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while (!done) { |
280 |
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loops++; |
281 |
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|
282 |
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// Pick a processor at random |
283 |
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|
284 |
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which_proc = (int) (myRandom.getRandom() * nProcessors); |
285 |
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|
286 |
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//get the molecule stamp first |
287 |
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int stampId = info->getMoleculeStampId(i); |
288 |
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MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId); |
289 |
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|
290 |
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// How many atoms does this processor have so far? |
291 |
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old_atoms = atomsPerProc[which_proc]; |
292 |
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add_atoms = moleculeStamp->getNAtoms(); |
293 |
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new_atoms = old_atoms + add_atoms; |
294 |
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|
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// If we've been through this loop too many times, we need |
296 |
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// to just give up and assign the molecule to this processor |
297 |
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// and be done with it. |
298 |
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|
299 |
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if (loops > 100) { |
300 |
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sprintf(painCave.errMsg, |
301 |
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"I've tried 100 times to assign molecule %d to a " |
302 |
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" processor, but can't find a good spot.\n" |
303 |
< |
"I'm assigning it at random to processor %d.\n", |
304 |
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i, which_proc); |
305 |
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|
306 |
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painCave.isFatal = 0; |
307 |
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simError(); |
308 |
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|
309 |
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molToProcMap[i] = which_proc; |
310 |
< |
atomsPerProc[which_proc] += add_atoms; |
311 |
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|
312 |
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done = 1; |
313 |
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continue; |
314 |
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} |
315 |
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|
316 |
< |
// If we can add this molecule to this processor without sending |
317 |
< |
// it above nTarget, then go ahead and do it: |
318 |
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|
319 |
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if (new_atoms <= nTarget) { |
320 |
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molToProcMap[i] = which_proc; |
321 |
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atomsPerProc[which_proc] += add_atoms; |
322 |
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|
323 |
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done = 1; |
324 |
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continue; |
325 |
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} |
326 |
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|
327 |
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// The only situation left is when new_atoms > nTarget. We |
328 |
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// want to accept this with some probability that dies off the |
329 |
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// farther we are from nTarget |
330 |
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|
331 |
< |
// roughly: x = new_atoms - nTarget |
332 |
< |
// Pacc(x) = exp(- a * x) |
333 |
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// where a = penalty / (average atoms per molecule) |
334 |
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|
335 |
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x = (double)(new_atoms - nTarget); |
336 |
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y = myRandom.getRandom(); |
337 |
< |
|
338 |
< |
if (y < exp(- a * x)) { |
339 |
< |
molToProcMap[i] = which_proc; |
340 |
< |
atomsPerProc[which_proc] += add_atoms; |
341 |
< |
|
342 |
< |
done = 1; |
343 |
< |
continue; |
344 |
< |
} else { |
345 |
< |
continue; |
346 |
< |
} |
347 |
< |
} |
348 |
< |
} |
349 |
< |
|
350 |
< |
// Spray out this nonsense to all other processors: |
351 |
< |
|
352 |
< |
MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
353 |
< |
} else { |
354 |
< |
|
355 |
< |
// Listen to your marching orders from processor 0: |
356 |
< |
|
357 |
< |
MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
270 |
> |
numerator = info->getNGlobalAtoms(); |
271 |
> |
denominator = nProcessors; |
272 |
> |
precast = numerator / denominator; |
273 |
> |
nTarget = (int)(precast + 0.5); |
274 |
> |
|
275 |
> |
for(i = 0; i < nGlobalMols; i++) { |
276 |
> |
done = 0; |
277 |
> |
loops = 0; |
278 |
> |
|
279 |
> |
while (!done) { |
280 |
> |
loops++; |
281 |
> |
|
282 |
> |
// Pick a processor at random |
283 |
> |
|
284 |
> |
which_proc = (int) (myRandom->rand() * nProcessors); |
285 |
> |
|
286 |
> |
//get the molecule stamp first |
287 |
> |
int stampId = info->getMoleculeStampId(i); |
288 |
> |
MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId); |
289 |
> |
|
290 |
> |
// How many atoms does this processor have so far? |
291 |
> |
old_atoms = atomsPerProc[which_proc]; |
292 |
> |
add_atoms = moleculeStamp->getNAtoms(); |
293 |
> |
new_atoms = old_atoms + add_atoms; |
294 |
> |
|
295 |
> |
// If we've been through this loop too many times, we need |
296 |
> |
// to just give up and assign the molecule to this processor |
297 |
> |
// and be done with it. |
298 |
> |
|
299 |
> |
if (loops > 100) { |
300 |
> |
sprintf(painCave.errMsg, |
301 |
> |
"I've tried 100 times to assign molecule %d to a " |
302 |
> |
" processor, but can't find a good spot.\n" |
303 |
> |
"I'm assigning it at random to processor %d.\n", |
304 |
> |
i, which_proc); |
305 |
> |
|
306 |
> |
painCave.isFatal = 0; |
307 |
> |
simError(); |
308 |
> |
|
309 |
> |
molToProcMap[i] = which_proc; |
310 |
> |
atomsPerProc[which_proc] += add_atoms; |
311 |
> |
|
312 |
> |
done = 1; |
313 |
> |
continue; |
314 |
> |
} |
315 |
> |
|
316 |
> |
// If we can add this molecule to this processor without sending |
317 |
> |
// it above nTarget, then go ahead and do it: |
318 |
> |
|
319 |
> |
if (new_atoms <= nTarget) { |
320 |
> |
molToProcMap[i] = which_proc; |
321 |
> |
atomsPerProc[which_proc] += add_atoms; |
322 |
> |
|
323 |
> |
done = 1; |
324 |
> |
continue; |
325 |
> |
} |
326 |
> |
|
327 |
> |
// The only situation left is when new_atoms > nTarget. We |
328 |
> |
// want to accept this with some probability that dies off the |
329 |
> |
// farther we are from nTarget |
330 |
> |
|
331 |
> |
// roughly: x = new_atoms - nTarget |
332 |
> |
// Pacc(x) = exp(- a * x) |
333 |
> |
// where a = penalty / (average atoms per molecule) |
334 |
> |
|
335 |
> |
x = (double)(new_atoms - nTarget); |
336 |
> |
y = myRandom->rand(); |
337 |
> |
|
338 |
> |
if (y < exp(- a * x)) { |
339 |
> |
molToProcMap[i] = which_proc; |
340 |
> |
atomsPerProc[which_proc] += add_atoms; |
341 |
> |
|
342 |
> |
done = 1; |
343 |
> |
continue; |
344 |
> |
} else { |
345 |
> |
continue; |
346 |
> |
} |
347 |
> |
} |
348 |
> |
} |
349 |
> |
|
350 |
> |
delete myRandom; |
351 |
> |
|
352 |
> |
// Spray out this nonsense to all other processors: |
353 |
> |
|
354 |
> |
MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
355 |
> |
} else { |
356 |
> |
|
357 |
> |
// Listen to your marching orders from processor 0: |
358 |
> |
|
359 |
> |
MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
360 |
|
} |
361 |
< |
|
361 |
> |
|
362 |
|
info->setMolToProcMap(molToProcMap); |
363 |
|
sprintf(checkPointMsg, |
364 |
|
"Successfully divided the molecules among the processors.\n"); |
365 |
|
MPIcheckPoint(); |
366 |
< |
} |
367 |
< |
|
366 |
> |
} |
367 |
> |
|
368 |
|
#endif |
369 |
< |
|
370 |
< |
void SimCreator::createMolecules(SimInfo *info) { |
369 |
> |
|
370 |
> |
void SimCreator::createMolecules(SimInfo *info) { |
371 |
|
MoleculeCreator molCreator; |
372 |
|
int stampId; |
373 |
< |
|
373 |
> |
|
374 |
|
for(int i = 0; i < info->getNGlobalMolecules(); i++) { |
375 |
< |
|
375 |
> |
|
376 |
|
#ifdef IS_MPI |
377 |
< |
|
378 |
< |
if (info->getMolToProc(i) == worldRank) { |
377 |
> |
|
378 |
> |
if (info->getMolToProc(i) == worldRank) { |
379 |
|
#endif |
380 |
< |
|
381 |
< |
stampId = info->getMoleculeStampId(i); |
382 |
< |
Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId), |
383 |
< |
stampId, i, info->getLocalIndexManager()); |
384 |
< |
|
385 |
< |
info->addMolecule(mol); |
386 |
< |
|
380 |
> |
|
381 |
> |
stampId = info->getMoleculeStampId(i); |
382 |
> |
Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId), |
383 |
> |
stampId, i, info->getLocalIndexManager()); |
384 |
> |
|
385 |
> |
info->addMolecule(mol); |
386 |
> |
|
387 |
|
#ifdef IS_MPI |
388 |
< |
|
389 |
< |
} |
390 |
< |
|
388 |
> |
|
389 |
> |
} |
390 |
> |
|
391 |
|
#endif |
392 |
< |
|
392 |
> |
|
393 |
|
} //end for(int i=0) |
394 |
< |
} |
395 |
< |
|
396 |
< |
void SimCreator::compList(MakeStamps *stamps, Globals* simParams, |
397 |
< |
std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) { |
394 |
> |
} |
395 |
> |
|
396 |
> |
void SimCreator::compList(MakeStamps *stamps, Globals* simParams, |
397 |
> |
std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) { |
398 |
|
int i; |
399 |
|
char * id; |
400 |
|
MoleculeStamp * currentStamp; |
401 |
|
Component** the_components = simParams->getComponents(); |
402 |
|
int n_components = simParams->getNComponents(); |
403 |
< |
|
403 |
> |
|
404 |
|
if (!simParams->haveNMol()) { |
405 |
< |
// we don't have the total number of molecules, so we assume it is |
406 |
< |
// given in each component |
405 |
> |
// we don't have the total number of molecules, so we assume it is |
406 |
> |
// given in each component |
407 |
> |
|
408 |
> |
for(i = 0; i < n_components; i++) { |
409 |
> |
if (!the_components[i]->haveNMol()) { |
410 |
> |
// we have a problem |
411 |
> |
sprintf(painCave.errMsg, |
412 |
> |
"SimCreator Error. No global NMol or component NMol given.\n" |
413 |
> |
"\tCannot calculate the number of atoms.\n"); |
414 |
> |
|
415 |
> |
painCave.isFatal = 1; |
416 |
> |
simError(); |
417 |
> |
} |
418 |
> |
|
419 |
> |
id = the_components[i]->getType(); |
420 |
|
|
421 |
< |
for(i = 0; i < n_components; i++) { |
422 |
< |
if (!the_components[i]->haveNMol()) { |
423 |
< |
// we have a problem |
424 |
< |
sprintf(painCave.errMsg, |
425 |
< |
"SimCreator Error. No global NMol or component NMol given.\n" |
426 |
< |
"\tCannot calculate the number of atoms.\n"); |
427 |
< |
|
428 |
< |
painCave.isFatal = 1; |
429 |
< |
simError(); |
430 |
< |
} |
431 |
< |
|
432 |
< |
id = the_components[i]->getType(); |
433 |
< |
currentStamp = (stamps->extractMolStamp(id))->getStamp(); |
464 |
< |
|
465 |
< |
if (currentStamp == NULL) { |
466 |
< |
sprintf(painCave.errMsg, |
467 |
< |
"SimCreator error: Component \"%s\" was not found in the " |
468 |
< |
"list of declared molecules\n", id); |
469 |
< |
|
470 |
< |
painCave.isFatal = 1; |
471 |
< |
simError(); |
472 |
< |
} |
473 |
< |
|
474 |
< |
moleculeStampPairs.push_back( |
475 |
< |
std::make_pair(currentStamp, the_components[i]->getNMol())); |
476 |
< |
} //end for (i = 0; i < n_components; i++) |
421 |
> |
currentStamp = stamps->getMolStamp(id); |
422 |
> |
if (currentStamp == NULL) { |
423 |
> |
sprintf(painCave.errMsg, |
424 |
> |
"SimCreator error: Component \"%s\" was not found in the " |
425 |
> |
"list of declared molecules\n", id); |
426 |
> |
|
427 |
> |
painCave.isFatal = 1; |
428 |
> |
simError(); |
429 |
> |
} |
430 |
> |
|
431 |
> |
moleculeStampPairs.push_back( |
432 |
> |
std::make_pair(currentStamp, the_components[i]->getNMol())); |
433 |
> |
} //end for (i = 0; i < n_components; i++) |
434 |
|
} else { |
435 |
< |
sprintf(painCave.errMsg, "SimSetup error.\n" |
436 |
< |
"\tSorry, the ability to specify total" |
437 |
< |
" nMols and then give molfractions in the components\n" |
438 |
< |
"\tis not currently supported." |
439 |
< |
" Please give nMol in the components.\n"); |
440 |
< |
|
441 |
< |
painCave.isFatal = 1; |
442 |
< |
simError(); |
435 |
> |
sprintf(painCave.errMsg, "SimSetup error.\n" |
436 |
> |
"\tSorry, the ability to specify total" |
437 |
> |
" nMols and then give molfractions in the components\n" |
438 |
> |
"\tis not currently supported." |
439 |
> |
" Please give nMol in the components.\n"); |
440 |
> |
|
441 |
> |
painCave.isFatal = 1; |
442 |
> |
simError(); |
443 |
|
} |
444 |
< |
|
444 |
> |
|
445 |
|
#ifdef IS_MPI |
446 |
< |
|
446 |
> |
|
447 |
|
strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
448 |
|
MPIcheckPoint(); |
449 |
< |
|
449 |
> |
|
450 |
|
#endif // is_mpi |
451 |
< |
|
452 |
< |
} |
453 |
< |
|
454 |
< |
void SimCreator::setGlobalIndex(SimInfo *info) { |
451 |
> |
|
452 |
> |
} |
453 |
> |
|
454 |
> |
void SimCreator::setGlobalIndex(SimInfo *info) { |
455 |
|
SimInfo::MoleculeIterator mi; |
456 |
|
Molecule::AtomIterator ai; |
457 |
|
Molecule::RigidBodyIterator ri; |
466 |
|
int nGlobalAtoms = info->getNGlobalAtoms(); |
467 |
|
|
468 |
|
#ifndef IS_MPI |
469 |
< |
|
469 |
> |
|
470 |
|
beginAtomIndex = 0; |
471 |
|
beginRigidBodyIndex = 0; |
472 |
|
beginCutoffGroupIndex = 0; |
473 |
< |
|
473 |
> |
|
474 |
|
#else |
475 |
< |
|
475 |
> |
|
476 |
|
int nproc; |
477 |
|
int myNode; |
478 |
< |
|
478 |
> |
|
479 |
|
myNode = worldRank; |
480 |
|
MPI_Comm_size(MPI_COMM_WORLD, &nproc); |
481 |
< |
|
481 |
> |
|
482 |
|
std::vector < int > tmpAtomsInProc(nproc, 0); |
483 |
|
std::vector < int > tmpRigidBodiesInProc(nproc, 0); |
484 |
|
std::vector < int > tmpCutoffGroupsInProc(nproc, 0); |
485 |
|
std::vector < int > NumAtomsInProc(nproc, 0); |
486 |
|
std::vector < int > NumRigidBodiesInProc(nproc, 0); |
487 |
|
std::vector < int > NumCutoffGroupsInProc(nproc, 0); |
488 |
< |
|
488 |
> |
|
489 |
|
tmpAtomsInProc[myNode] = info->getNAtoms(); |
490 |
|
tmpRigidBodiesInProc[myNode] = info->getNRigidBodies(); |
491 |
|
tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups(); |
492 |
< |
|
492 |
> |
|
493 |
|
//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups |
494 |
|
MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT, |
495 |
|
MPI_SUM, MPI_COMM_WORLD); |
497 |
|
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
498 |
|
MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc, |
499 |
|
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
500 |
< |
|
500 |
> |
|
501 |
|
beginAtomIndex = 0; |
502 |
|
beginRigidBodyIndex = 0; |
503 |
|
beginCutoffGroupIndex = 0; |
504 |
< |
|
504 |
> |
|
505 |
|
for(int i = 0; i < myNode; i++) { |
506 |
< |
beginAtomIndex += NumAtomsInProc[i]; |
507 |
< |
beginRigidBodyIndex += NumRigidBodiesInProc[i]; |
508 |
< |
beginCutoffGroupIndex += NumCutoffGroupsInProc[i]; |
506 |
> |
beginAtomIndex += NumAtomsInProc[i]; |
507 |
> |
beginRigidBodyIndex += NumRigidBodiesInProc[i]; |
508 |
> |
beginCutoffGroupIndex += NumCutoffGroupsInProc[i]; |
509 |
|
} |
510 |
< |
|
510 |
> |
|
511 |
|
#endif |
512 |
< |
|
512 |
> |
|
513 |
> |
//rigidbody's index begins right after atom's |
514 |
> |
beginRigidBodyIndex += info->getNGlobalAtoms(); |
515 |
> |
|
516 |
|
for(mol = info->beginMolecule(mi); mol != NULL; |
517 |
|
mol = info->nextMolecule(mi)) { |
518 |
< |
|
519 |
< |
//local index(index in DataStorge) of atom is important |
520 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
521 |
< |
atom->setGlobalIndex(beginAtomIndex++); |
522 |
< |
} |
523 |
< |
|
524 |
< |
for(rb = mol->beginRigidBody(ri); rb != NULL; |
525 |
< |
rb = mol->nextRigidBody(ri)) { |
526 |
< |
rb->setGlobalIndex(beginRigidBodyIndex++); |
527 |
< |
} |
528 |
< |
|
529 |
< |
//local index of cutoff group is trivial, it only depends on the order of travesing |
530 |
< |
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
531 |
< |
cg = mol->nextCutoffGroup(ci)) { |
532 |
< |
cg->setGlobalIndex(beginCutoffGroupIndex++); |
533 |
< |
} |
518 |
> |
|
519 |
> |
//local index(index in DataStorge) of atom is important |
520 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
521 |
> |
atom->setGlobalIndex(beginAtomIndex++); |
522 |
> |
} |
523 |
> |
|
524 |
> |
for(rb = mol->beginRigidBody(ri); rb != NULL; |
525 |
> |
rb = mol->nextRigidBody(ri)) { |
526 |
> |
rb->setGlobalIndex(beginRigidBodyIndex++); |
527 |
> |
} |
528 |
> |
|
529 |
> |
//local index of cutoff group is trivial, it only depends on the order of travesing |
530 |
> |
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
531 |
> |
cg = mol->nextCutoffGroup(ci)) { |
532 |
> |
cg->setGlobalIndex(beginCutoffGroupIndex++); |
533 |
> |
} |
534 |
|
} |
535 |
< |
|
535 |
> |
|
536 |
|
//fill globalGroupMembership |
537 |
|
std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0); |
538 |
|
for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
539 |
< |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
540 |
< |
|
541 |
< |
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
542 |
< |
globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex(); |
543 |
< |
} |
544 |
< |
|
545 |
< |
} |
539 |
> |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
540 |
> |
|
541 |
> |
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
542 |
> |
globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex(); |
543 |
> |
} |
544 |
> |
|
545 |
> |
} |
546 |
|
} |
547 |
< |
|
547 |
> |
|
548 |
|
#ifdef IS_MPI |
549 |
|
// Since the globalGroupMembership has been zero filled and we've only |
550 |
|
// poked values into the atoms we know, we can do an Allreduce |
554 |
|
std::vector<int> tmpGroupMembership(nGlobalAtoms, 0); |
555 |
|
MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms, |
556 |
|
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
557 |
< |
info->setGlobalGroupMembership(tmpGroupMembership); |
557 |
> |
info->setGlobalGroupMembership(tmpGroupMembership); |
558 |
|
#else |
559 |
|
info->setGlobalGroupMembership(globalGroupMembership); |
560 |
|
#endif |
561 |
< |
|
561 |
> |
|
562 |
|
//fill molMembership |
563 |
|
std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0); |
564 |
|
|
565 |
|
for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
566 |
< |
|
567 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
568 |
< |
globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex(); |
569 |
< |
} |
566 |
> |
|
567 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
568 |
> |
globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex(); |
569 |
> |
} |
570 |
|
} |
571 |
< |
|
571 |
> |
|
572 |
|
#ifdef IS_MPI |
573 |
|
std::vector<int> tmpMolMembership(nGlobalAtoms, 0); |
574 |
< |
|
574 |
> |
|
575 |
|
MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms, |
576 |
|
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
577 |
|
|
579 |
|
#else |
580 |
|
info->setGlobalMolMembership(globalMolMembership); |
581 |
|
#endif |
582 |
< |
|
583 |
< |
} |
584 |
< |
|
585 |
< |
void SimCreator::loadCoordinates(SimInfo* info) { |
582 |
> |
|
583 |
> |
} |
584 |
> |
|
585 |
> |
void SimCreator::loadCoordinates(SimInfo* info) { |
586 |
|
Globals* simParams; |
587 |
|
simParams = info->getSimParams(); |
588 |
|
|
589 |
|
if (!simParams->haveInitialConfig()) { |
590 |
< |
sprintf(painCave.errMsg, |
591 |
< |
"Cannot intialize a simulation without an initial configuration file.\n"); |
592 |
< |
painCave.isFatal = 1;; |
593 |
< |
simError(); |
590 |
> |
sprintf(painCave.errMsg, |
591 |
> |
"Cannot intialize a simulation without an initial configuration file.\n"); |
592 |
> |
painCave.isFatal = 1;; |
593 |
> |
simError(); |
594 |
|
} |
595 |
< |
|
595 |
> |
|
596 |
|
DumpReader reader(info, simParams->getInitialConfig()); |
597 |
|
int nframes = reader.getNFrames(); |
598 |
< |
|
598 |
> |
|
599 |
|
if (nframes > 0) { |
600 |
< |
reader.readFrame(nframes - 1); |
600 |
> |
reader.readFrame(nframes - 1); |
601 |
|
} else { |
602 |
< |
//invalid initial coordinate file |
603 |
< |
sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n", |
604 |
< |
simParams->getInitialConfig()); |
605 |
< |
painCave.isFatal = 1; |
606 |
< |
simError(); |
602 |
> |
//invalid initial coordinate file |
603 |
> |
sprintf(painCave.errMsg, |
604 |
> |
"Initial configuration file %s should at least contain one frame\n", |
605 |
> |
simParams->getInitialConfig()); |
606 |
> |
painCave.isFatal = 1; |
607 |
> |
simError(); |
608 |
|
} |
609 |
< |
|
609 |
> |
|
610 |
|
//copy the current snapshot to previous snapshot |
611 |
|
info->getSnapshotManager()->advance(); |
612 |
< |
} |
613 |
< |
|
612 |
> |
} |
613 |
> |
|
614 |
|
} //end namespace oopse |
615 |
|
|
616 |
|
|